{ "uniprot_canonical_ac": "A0A599-1", "ptm_annotation": [], "sequence": { "header": "sp|A0A599-1|TVB56_HUMAN Isoform 1 of T cell receptor beta variable 5-6 OS=Homo sapiens OX=9606 GN=TRBV5-6 PE=3 SV=1 CANONICAL=A0A599-1", "length": 114, "sequence": "MGPGLLCWALLCLLGAGLVDAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSL" }, "uniprot_id": "TVB56_HUMAN", "enzyme_annotation": [], "glycation": [], "keywords": [ "glycoprotein", "predicted.uniprotkb_gly" ], "species": [ { "common_name": "Human", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "name": "Homo sapiens", "taxid": 9606 } ], "publication": [ { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/15040585", "type": [ "PubMed" ], "id": "15040585" } ], "title": "The many important facets of T-cell repertoire diversity.", "journal": "Nat. Rev. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "authors": "Messaoudi I., Nikolich-Zugich J., Slifka M.K.", "date": "2004" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/20452950", "type": [ "PubMed" ], "id": "20452950" } ], "title": "Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling.", "journal": "Cold Spring Harb. Perspect. Biol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "authors": "Gagnon E., Wucherpfennig K.W., Call M.E., Call M.J., Huseby E.S.", "date": "2010" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/23524462", "type": [ "PubMed" ], "id": "23524462" } ], "title": "T cell receptor signalling networks: branched, diversified and bounded.", "journal": "Nat. Rev. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "authors": "Zamoyska R., Brownlie R.J.", "date": "2013" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/24600447", "type": [ "PubMed" ], "id": "24600447" } ], "title": "Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics.", "journal": "Front. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "authors": "Lefranc M.P.", "date": "2014" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/25493333", "type": [ "PubMed" ], "id": "25493333" } ], "title": "T cell antigen receptor recognition of antigen-presenting molecules.", "journal": "Annu. Rev. Immunol.", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "authors": "Rossjohn J., Gras S., McCluskey J., Godfrey D.I., Miles J.J., Turner S.J.", "date": "2015" }, { "reference": [ { "url": "https://www.ncbi.nlm.nih.gov/pubmed/8650574", "type": [ "PubMed" ], "id": "8650574" } ], "title": "The complete 685-kilobase DNA sequence of the human beta T cell receptor locus.", "journal": "Science", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "id": "A0A599", "database": "UniProtKB" } ], "authors": "Hood L., Koop B.F., Rowen L.", "date": "1996" } ], "uniprot_ac": "A0A599", "site_annotation": [ { "end_pos": 92, "annotation": "n_glycosylation_sequon", "start_pos": 90 } ], "isoforms": [ { "url": "https://www.uniprot.org/uniprot/A0A599#A0A599-1", "isoform_ac": "A0A599-1", "locus": { "end_pos": 142500069, "strand": "-", "start_pos": 142500533, "chromosome": "7", "evidence": [ { "url": "https://www.ensembl.org/id/ENST00000390375", "id": "ENST00000390375", "database": "Ensembl Transcript" }, { "url": "https://www.ensembl.org/id/ENSP00000374898", "id": "ENSP00000374898", "database": "Ensembl Peptide" } ] }, "sequence": { "header": "sp|A0A599-1|TVB56_HUMAN Isoform 1 of T cell receptor beta variable 5-6 OS=Homo sapiens OX=9606 GN=TRBV5-6 PE=3 SV=1 CANONICAL=A0A599-1", "length": 114, "sequence": "MGPGLLCWALLCLLGAGLVDAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSL" } } ], "pathway": [], "function": [ { "url": "https://www.uniprot.org/uniprot/A0A599#function", "annotation": "V region of the variable domain of T cell receptor (TR) beta chain that participates in the antigen recognition (PubMed:24600447). Alpha-beta T cell receptors are antigen specific receptors which are essential to the immune response and are present on the cell surface of T lymphocytes. Recognize peptide-major histocompatibility (MH) (pMH) complexes that are displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens (PubMed:25493333). Binding of alpha-beta TR to pMH complex initiates TR-CD3 clustering on the cell surface and intracellular activation of LCK that phosphorylates the ITAM motifs of CD3G, CD3D, CD3E and CD247 enabling the recruitment of ZAP70. In turn ZAP70 phosphorylates LAT, which recruits numerous signaling molecules to form the LAT signalosome. The LAT signalosome propagates signal branching to three major signaling pathways, the calcium, the mitogen-activated protein kinase (MAPK) kinase and the nuclear factor NF-kappa-B (NF-kB) pathways, leading to the mobilization of transcription factors that are critical for gene expression and essential for T cell growth and differentiation (PubMed:23524462). The T cell repertoire is generated in the thymus, by V-(D)-J rearrangement. This repertoire is then shaped by intrathymic selection events to generate a peripheral T cell pool of self-MH restricted, non-autoaggressive T cells. Post-thymic interaction of alpha-beta TR with the pMH complexes shapes TR structural and functional avidity (PubMed:15040585).", "evidence": [ { "url": "https://www.uniprot.org/uniprot/A0A599#function", "id": "A0A599", "database": "UniProtKB" } ] } ], "orthologs": [], "interactions": [], "synthesized_glycans": [], "snv": [ { "sequence_org": "A", "start_pos": 16, "alt_nt": "T", "chr_id": "7", "ref_nt": "C", "chr_pos": "142131832", "disease": [ { "synonyms": [ { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "malignant hematopoietic neoplasm", "description": "" } ], "recommended_name": { "id": "DOID:2531", "url": "http://disease-ontology.org/term/DOID:2531", "resource": "Disease Ontology", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." } }, { "synonyms": [ { "id": "DOID:1781", "url": "http://disease-ontology.org/term/DOID:1781", "resource": "Disease Ontology", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "url": "http://disease-ontology.org/term/DOID:1781", "resource": "Disease Ontology", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "url": "http://disease-ontology.org/term/DOID:1781", "resource": "Disease Ontology", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "url": "http://disease-ontology.org/term/DOID:1781", "resource": "Disease Ontology", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "url": "http://disease-ontology.org/term/DOID:1781", "resource": "Disease Ontology", "name": "thyroid neoplasm", "description": "" } ], "recommended_name": { "id": "DOID:1781", "url": "http://disease-ontology.org/term/DOID:1781", "resource": "Disease Ontology", "name": "thyroid gland cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage." } } ], "evidence": [ { "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/A0A599", "id": "A0A599", "database": "BioMuta" } ], "glycoeffect": [], "frequency": "1.6", "sequence_mut": "T", "subjects_tested": "125", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "annotation": "Somatic mutation passed 1 out of 6 filters: patient freq. (1.6%).", "end_pos": 16, "minor_allelic_frequency": "", "subjects_positive": "2" }, { "sequence_org": "I", "alt_nt": "null", "chr_id": "7", "ref_nt": "A", "chr_pos": "142500283T>", "evidence": [ { "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762750366", "id": "rs762750366", "database": "dbSNP" }, { "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762750366", "id": "rs762750366", "database": "ExAC" }, { "url": "http://gnomad.broadinstitute.org/awesome?query=rs762750366", "id": "rs762750366", "database": "gnomAD" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_mut": "N", "start_pos": 31, "keywords": [ "ebi", "germline" ], "end_pos": 31, "minor_allelic_frequency": "", "annotation": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (IKT->NKT)." }, { "sequence_org": "P", "start_pos": 80, "alt_nt": "A", "chr_id": "7", "ref_nt": "G", "chr_pos": "142131517", "disease": [ { "synonyms": [ { "id": "DOID:4159", "url": "http://disease-ontology.org/term/DOID:4159", "resource": "Disease Ontology", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "url": "http://disease-ontology.org/term/DOID:4159", "resource": "Disease Ontology", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "url": "http://disease-ontology.org/term/DOID:4159", "resource": "Disease Ontology", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "recommended_name": { "id": "DOID:4159", "url": "http://disease-ontology.org/term/DOID:4159", "resource": "Disease Ontology", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." } } ], "evidence": [ { "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/A0A599", "id": "A0A599", "database": "BioMuta" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "frequency": "0.2", "sequence_mut": "S", "subjects_tested": "820", "keywords": 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], "mutagenesis": [], "disease": [], "phosphorylation": [], "mass": { "monoisotopic_mass": 12565.0, "chemical_mass": 12565.0 }, "expression_tissue": [], "gene": [ { "url": "https://www.uniprot.org/uniprot/A0A599", "name": "TRBV5-6", "locus": { "end_pos": 142500534, "strand": "+", "start_pos": 142500028, "chromosome": "7", "evidence": [ { "url": "https://www.ensembl.org/id/ENSG00000211728", "id": "ENSG00000211728", "database": "Ensembl Gene" } ] } } ], "protein_names": [ { "url": "https://www.uniprot.org/uniprot/A0A599#names_and_taxonomy", "type": "recommended", "resource": "UniProtKB", "name": "T cell receptor beta variable 5-6" } ] }